It's that Mecca-Medina contradiction in Muhammad's actions and preachings. He became a full blown psycho killer in Medina.
The "nice" Muslims only quote the "nice" parts of the Koran and ignore (to varying degrees) the murderous imprecations in it. In Koran and Hadith. They will lie to you and tell you Jihad means only inner struggle, not war.
If I hear that inner struggle bull crap to rationalize...arrrrgh...drives me freaking nuts.